The Plant Genome Integrative Explorer Resource: PlantGenIE.org. Issue 4 (20th July 2015)

• Record Type: Journal Article
• Authors: Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao‐Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R.; Street, Nathaniel R.
• Is Part Of: New phytologist. Volume 208:Issue 4(2015:Dec. 15)
• Page Start: 1149
• Page End: 1156
• Publication Date: 2015-07-20
• Subjects: annotation -- coexpression -- conifer -- database -- genome browser -- Populus -- transcriptomics -- web resource; Botany -- Periodicals; 580
• DOI: 10.1111/nph.13557
• Languages: English
• ISSNs: 0028-646X

Abstract

Summary: Accessing and exploring large‐scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA‐sequencing (RNA‐Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the Com Pl Ex resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large‐scale and genome‐wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.